title: CTV-1_PU.1mRNA_FA_PU.1-ChIP_1


title: DMSO_input_rep1

status: Public on Nov 17 2019

type: SRA

city: Berkeley

first: Xavier

last: Darzacq

state: CA

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

country: USA

institute: University of California, Berkeley

library_source: genomic

data_processing:
Base-calling performed with CASAVA by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 with --very-sensitive-local
bigWig coverage files were generated with deepTools with the following configurations: --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2308125349 --ignoreDuplicates --ignoreForNormalization chrX chrY chrM
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: JM8.N4 mouse embryonic stem cells were grown on plates pre-coated with a 0.1% autoclaved gelatin solution (Sigma-Aldrich, G9391) under feeder free condition in knock-out DMEM with 15% FBS and LIF (full recipe: 500 mL DMEM (ThermoFisher#10829018), 6 mL MEM NEAA (ThermoFisher #11140050), 6 mL GlutaMax (ThermoFisher#35050061), 5 mL Penicillin-streptomycin (ThermoFisher #15140122), 4.6 μL 2-mercapoethanol (Sigma-Aldrich M3148), 90 mL fetal bovine serum (HyClone FBS SH30910.03 lot #AXJ47554)). mES cells were fed by replacing half the medium with fresh medium daily and passaged every two days by trypsinization.

extract_protocol:
Cell pellets were thawed in ice and resuspended in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40, 1 ml/15 cm plate) and incubated for 10 min on ice. Lysates were then centrifuged for 10 min at 4000 rpm. Nuclear pellets were resuspended in 6 volumes of sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 0.1% SDS), incubated on ice for 10 min, and sonicated to obtain DNA fragments below 2000 bp in length (Covaris S220 sonicator, 20% Duty factor, 200 cycles/burst, 100 peak incident power, 25 cycles of 20" on and 40" off). Sonicated lysates were cleared by centrifugation and 1 mg of chromatin was diluted in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) to a final concentration of 0.8 μg/μl, precleared with Protein A sepharose (GE Healthcare) for 2 hours at 4°C and immunoprecipitated overnight with 10 μg of antibodies. 4% of the precleared chromatin was saved as input. Immunoprecipitated DNA was purified with the Qiagen QIAquick PCR Purification Kit, eluted in 40 μl of water and used for library preparation.
Solexa rapid prep (see linked manuscript).

treatment_protocol: Cells were treated with DMSO for 45 minutes and cross-linked for 6 minutes at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final). Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10 min at 4000 rpm, 4 'C and pellets flash-frozen in liquid nitrogen and stored at - 80 'C until lysed.

tag: cell line

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: Wild-type with DMSO treatment

tag: chip antibody


title: HEPG2_PU1mut_1

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

description: Cells were transfected with IVT mRNA and transposition was carried out 8 hours after transfection

data_processing:
Raw data were aligned to the human genome (GRCh37/hg19) using bowtie2 in very-sensitive and no-discordant modes, keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10). Read positions were adjusted to move the ends proximal to the Tn5 binding site (for reads on the positive strand, the start is shifted +4 bp and its partner reads start -5 bp, for reads on the negative strand, the start is shifted -5 bp and its partner reads start +4 bp) using a custom script.
Bigwigs of ChIPseq data sets were generated using HOMER v4.9 (Heinz et al, 2010) and a fixed fragment length of 65 bp. For cancer cell lines, we used the Control-FREEC v11.0 program to determine allelic imbalances from low-depth whole genome sequencing data and corrected ChIP-seq read counts accordingly to generate CNV-corrected bigWigs.
ATAC-seq peak regions were called by combining two different approaches: The basic peak region set was called using HOMER?s findPeaks program in ?region?? mode using parameters ?-size 150 -minDist 250 -L 2 -fdr 0.00001? to identify regions of variable length by stitching nucleosome-size peaks. To exclude shallow peak regions, only those were kept that overlapped a second peak set that was generated in ??factor?? mode using parameters ?-size 250 -minDist 250 -L 2 -fdr 0.00001? to identify focal peaks.
Genome_build: hg19hg19
Supplementary_files_format_and_content: coverage tracks in bigWig format (before and after CNV normalization
Supplementary_files_format_and_content: ATACseq peaks (open chromatin regions)

organism: Homo sapiens

growth_protocol: CTV-1 and HEP-G2 cells were cultured in RPMI 1640 (Gibco; routinely supplemented with 2 mM L-glutamine (Biochrom), 1 mM sodium pyruvate (Sigma), 50 U/ml penicillin/streptomycin, 0.4x vitamins (Sigma), 1x non-essential amino acids (Sigma), 50 μM b-mercaptoethanol (Gibco)) supplemented with 10% heat inactivated fetal bovine serum; For TALL-1 cells the culture medium was supplemented with 15% heat inactivated fetal bovine serum was used; adherent HEP-G2 cells were detached using Trypsin-EDTA (Gibco)

extract_protocol:
Cells were treated with DNase I directly in culture medium prior to nuclear transposition procedure.
ATACseq was  essentially done as described (Corces et al. 2017).

treatment_protocol: Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA, PU1-delA-IVT-mRNA) and cultured for 8 hours prior to lysis procedure.

value: hepatocellular carcinoma cell line

tag: transfected ivt mrna

tag: molecule subtype

value: transposed, nuclear DNA


title: Pol2i_FLV_rep3

data_processing:
Library strategy: Micro-C
Base-calling performed with CASAVA by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley
allValidPairs were generated by HiC-Pro package (>2.10 version)
mcool files were converted from allValidPairs by Cooler package
hic file were converted from allValidPairs by Juicer tools
Genome_build: mm10
Supplementary_files_format_and_content: allValidParis file contains 1) read name, 2) chromosome of first locus, 3) read position of first locus, 4) strand of first locus, 5) chromosome of second locus, 6) read position of second locus, 7) strand of second locus, 8) DNA fragment length, 9) name of first restriction fragment, 10) name of second restriction fragment, 11) mapping quality of first read, 12) mapping quality of second read.
Supplementary_files_format_and_content: mcool file contains all valid Micro-C pairs stored in HDF5 format with multiple resolutions
Supplementary_files_format_and_content: hic file contains all valid Micro-C pairs with multiple resolutions

extract_protocol:
Micro-C protocol was performed as the following steps: 1) digest crosslinked chromatin by MNase; 2) Repair fragment ends with biotin-dNTP; 3) Proximal ligation and purge unligated ends; 4) Purify ligated dinucleosomal DNA.
Purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne™ Streptavidin C1. Standard library preparation protocol including end-repair, A-tailing, and adapter ligation was performed on beads with individual enzymes purchased from Lucigen or NEBnext UltraII kit. Sequencing library was amplified by Kapa HiFi PCR enzyme with lowest possible cycles to reduce PCR duplicates. Sequencing library was sequenced paired-end 50x50 in Illumina HiSeq 4000 sequencer.

treatment_protocol: Cells were treated with 2 µM flavopiridol (in DMSO) for 45 minutes and crosslinked by 1% formaldehyde for 10 min at room temperature. Formaldehyde reaction was quenched by 0.75M Tris. After two times of PBS washes, cells were then crosslinked by 3mM DSG for 45 min at room temperature. After two times of PBS washed, cell pellets were snap frozen or subjected to the following protocols.

value: Wild-type with Flavopiridol treatment


title: NEU_Input-ChIP_donorE

description: Chromatin input (control)

data_processing:
Raw data were aligned to the human genome (GRCh37/hg19) using bowtie2 (Langmead and Salzberg, 2012) in very sensitive mode, keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10).
Bigwigs of ChIPseq data sets were generated using HOMER v4.9 (Heinz et al, 2010) and standard settings. For cancer cell lines, we used the Control-FREEC v11.0 program to determine allelic imbalances from low-depth whole genome sequencing data and corrected ChIP-seq read counts accordingly to generate CNV-corrected bigWigs.
ChIP-seq peaks were called using HOMER?s findPeaks program in ??factor?? mode using default parameters (standard) or with -fdr 0.00001 (stringent) to identify focal peaks. Stringent peaks were further filtered for a minimal normalized tag count of 15 tags per peak. All peak sets were filtered by subtracting blacklisted genomic regions 49, and by filtering out regions with a mappability <0.8. The latter was annotated to peak regions from mappability tracks generated with the GEM package using HOMER?s annotatePeaks.pl.
Genome_build: hg19
Supplementary_files_format_and_content: ChIPseq tracks in bigWig format (before and after CNV normalization
Supplementary_files_format_and_content: ChIPseq peaks (called using standard or stringent parameters)

growth_protocol:
Neutrophils were purified from whole blood after lysis of erythrocytes and purified by FACS based on size and granularity.
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).

extract_protocol:
ChIPseq was essentially done as described (Pham et al. 2012).
Libraries were generated as described (Pham et al. 2012)

tag: donr id

value: donorE

tag: tissue/cell type

value: peripheral blood

tag: cell subtype

value: primary neutrophils


title: ncMO_PU.1-ChIP_donorD

description: Chromatin IP against PU.1

growth_protocol:
Peripheral blood monocytes were separated by leukapheresis of healthy donors, followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge (Beckman, München, Germany). The monocyte-enriched cell fraction was further subdivided by FACS (using BDs FACSAria) after staining with CD2-PE (RPA-2.10), CD15-PE (HI98), CD19-PE (4G7), CD56-PE (B159), NKp46-PE (9E2), to exclude remaining lymphocytes and granulocytes, as well as CD14-V450 (MΦP9) and CD16-Alexa647 (3G8) antibodies (all from BD). Monocytes were sorted into CD14++CD16– ("classical" subset) and CD14dimCD16+ cells ("nonclassica"l subset).
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).

value: donorD

value: primary monocytes

value: PU.1 (Santa Cruz, #sc-352X)


title: CTV-1_PU.1mRNA_FA_FLAG-ChIP_3

description: Chromatin IP against FLAG-epitope, 8h after mRNA transfection

extract_protocol:
Lysates were  preparated from sonicated nuclei and protein/histone-DNA complexes were isolated with antibody.
ChIP construction was essentially done as described (Pham et al. 2012) with slight modifications for BRG1, ETS1 and FLI1 samples, which were prepared using dual crosslinking with 2 mM DSG (Thermo Fisher Scientific) and 1% formaldehyde. Libraries for sequencing were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer’s instructions.

treatment_protocol: Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA, PU1-delA-IVT-mRNA, PU1-delQ-IVT-mRNA, PU1-delP-IVT-mRNA, PU1-delAQP-IVT-mRNA) and cultured for 8 hours prior to chromatin extraction

value: T cell leukemia cell line

value: FLAG M2 (Sigma, #F3165)

tag: fixation method

value: FA

tag: preperation batch


title: Pol2i_TRP_rep2

treatment_protocol: Cells were treated with 1 µM triptolide (in DMSO) for 45 minutes and crosslinked by 1% formaldehyde for 10 min at room temperature. Formaldehyde reaction was quenched by 0.75M Tris. After two times of PBS washes, cells were then crosslinked by 3mM DSG for 45 min at room temperature. After two times of PBS washed, cell pellets were snap frozen or subjected to the following protocols.

value: Wild-type with Tripotolide treatment


title: HEPG2_PU1_2


title: NEU_PU.1-ChIP_donorE

description: Chromatin IP against PU.1


title: TALL1_PU1mut_2


title: TALL1_PU1mut_1


title: Lung metastases rep4

city: New York

first: Wei

last: Zheng

state: NY

address: 1468 Madison Ave, Annenberg Building, Room 24-60A

institute: Icahn School of Medicine at Mount Sinai

description: processed data file: genes_fpkm.txt

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the mouse reference genome (mm10) using the Tophat (v2.0.13).
Gene models of Refgene were downloaded from the UCSC genome browser on March 13, 2017. FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were generated using the Cufflinks (v2.2.1). Lowly expressed genes (mean FPKM values < 1 in both groups under comparison) were excluded from differential expression analysis.
Read counts were obtained using HTSeq (v0.6.1).
DESeq2 (v1.6.3) was used to determine differentially expressed genes.
Genes with >2 fold change, false discovery rate (FDR) < 0.05, and FPKM>1 were identified as significantly differentially expressed.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *tsv: Tab-delimited gene expression values (read counts from HTseq).
Supplementary_files_format_and_content: genes_fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.

molecule: total RNA

source_name: FACS-sorted lung cells

extract_protocol:
Lung metastases were induced by tail vein injection of 1 x 10e6 E0771-LG to syngenic C57BL6/J female mice (6-8 wk old). Lungs were perfused with PBS through the right ventricle, dissected and minced. Lung metastases (<1 mm in diameter) were dissected with aid of a dissection microscope and pooled from 2-4 mice. The tissues were then digested with an enzyme mix of Liberase DL (Sigma-Aldrich 5466202001, 0.52 U/mL) and TL (Sigma-Aldrich 5401020001, 0.26 U/mL) and DNase I (Sigma-Aldrich DN25, 150 µg/mL) diluted in basal DMEM medium with rotation for 30 min at 37°C and filtered (70-µm member). Transcription inhibitors alpha-amanitin (Sigma-Aldrich A2263, 5 µg/mL) and actinomycin D (Sigma-Aldrich A1410, 1 µg/mL) were also added in the digestion buffer. Red blood cells were removed by incubation with RBC lysis buffer (Biolegend, 420301) for 5 min on ice (once for tissues and twice for blood). Cells were stained with Zombie Yellow to distinguish live/dead cells and were blocked with anti-mouse CD16/CD32 antibody (BD Biosciences 553141) for 10 min on ice, followed by staining with CD31 (BD Biosciences 563356) and CD45 (BD Biosciences 559864). CD31+/CD45- cells were sorted directly into the Extraction Buffer in the Picopure RNA isolation kit (Arcturus KIT0202) for isolation.
RNA sequencing of mouse total RNA was performed at Beijing Genomic Institute, using the Ovation® RNA-Seq System V2 kit for library construction, pair-end 100 bp and Hiseq 4000, which generated 60-80M reads per sample.

tag: tissue

value: Lung metastases

tag: cell population

tag: age

value: 8-10 weeks

tag: strain/background

value: Wild type


title: MAC7d_Input-ChIP_donorP

description: Chromatin input (control)

growth_protocol:
Peripheral blood monocytes were separated by leukapheresis of healthy donors, followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge. Monocytes were > 85% pure as determined by morphology and expression of CD14 antigen. To generate macrophages, isolated monocytes were cultured in endotoxin-free RPMI 1640 medium supplemented with vitamins, antibiotics, pyruvate, nonessential amino acids, 5 x 10-8 M beta-mercaptoethanol, 2% human pooled AB-group serum on teflon foils for 7 days.
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).

value: donorP

value: MO-derived

value: primary monocyte-derived macrophages


title: HEPG2_PU1_1

value: hepatocellular carcinoma cell line

value: transposed, nuclear DNA


title: Pol2i_TRP_rep3

value: embryonic stem cells


title: MAC7d_PU.1-ChIP_donorP

description: Chromatin IP against PU.1


title: ncMO_PU.1-ChIP_donorA

description: Chromatin IP against PU.1

value: donorA

value: peripheral blood


title: Lung metastases rep5

description: processed data file: genes_fpkm.txt


title: Lung metastases rep2

description: processed data file: genes_fpkm.txt


title: cMO_PU.1-ChIP_donorD

description: Chromatin IP against PU.1

value: donorD

value: primary monocytes


title: CTV1_PU1_delA_4

value: T cell leukemia cell line


title: cMO_PU.1-ChIP_donorA

description: Chromatin IP against PU.1

value: PU.1 (Santa Cruz, #sc-352X)


title: DO_HDACi rep1

city: Beijing

first: Huarong

last: Wang

address: NO. 2 Yuanmingyuan West Road

country: China

institute: China Agriculture University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: RPKM

source_name: Ovarian oocytes

extract_protocol:
Ovaries were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The denude oocytes were extracted from the wild type mice were treated with HDACi 4b or DMSO as negative control.

tag: strain background

value: wild type

value: post natal day 24

tag: treatment

value: HDACi 4b

value: ovary

value: denude oocytes


title: TALL1_PU1_1


title: TALL1_PU1_2


title: CTV-1_PU.1mRNA_FA_FLAG-ChIP_2

tag: cell line

value: FLAG M2 (Sigma, #F3165)

value: FA


title: MAC7d_PU.1-ChIP_donorN

description: Chromatin IP against PU.1

value: donorN

value: MO-derived

value: primary monocyte-derived macrophages


title: CTV1_PU1mut_5

tag: cell type

value: transposed, nuclear DNA


title: DO_HDACi rep2

tag: genotype/variation


title: Lung metastases rep3

description: processed data file: genes_fpkm.txt

value: Lung metastases

value: 8-10 weeks

value: Wild type


title: DO_CON rep1

value: control; DMSO


title: CTV1_PU1mut_4

value: T cell leukemia cell line


title: CTV1_PU1_delA_5


title: CTV1_PU1mut_3


title: Normal lung rep4

description: processed data file: genes_fpkm.txt

value: Normal lung


title: DO_CON rep2

value: wild type


title: Normal lung rep5

description: processed data file: genes_fpkm.txt


title: MAC7d_PU.1-ChIP_donorO

description: Chromatin IP against PU.1

value: donorO

tag: chip antibody

value: PU.1 (Santa Cruz, #sc-352X)


title: MO18h_PU.1-ChIP_donorO

description: Chromatin IP against PU.1

growth_protocol:
Peripheral blood monocytes were separated by leukapheresis of healthy donors, followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge. Monocytes were > 85% pure as determined by morphology and expression of CD14 antigen. Isolated monocytes were cultured in endotoxin-free RPMI 1640 medium supplemented with vitamins, antibiotics, pyruvate, nonessential amino acids, 5 x 10-8 M beta-mercaptoethanol, 2% human pooled AB-group serum on teflon foils for 18 hours.
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).

value: peripheral blood

value: primary monocytes


title: CTV-1_PU.1mRNA_FA_FLAG-ChIP_1

value: FLAG M2 (Sigma, #F3165)

tag: transfected ivt mrna


title: con-rep2

source_name: con_Ovarian granulosa cells

extract_protocol:
Ovaries were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A single i.p. injection of tamoxifen (20 mg/kg body weight) was administered respectively to 18-day-old Hdac3flox/flox; Foxl2-CreERT2 female mice and Hdac3flox/flox female mice (controls).

value: con

value: post natal day 24

value: ovary

value: Ovarian granulosa cells


title: HDACi 4b-rep2

source_name: HDACi 4b_Ovarian granulosa cells

value: HDACi 4b


title: HDACi 4b-rep1


title: MO4hLPS_PU.1-ChIP_donorO

description: Chromatin IP against PU.1

growth_protocol:
Peripheral blood monocytes were separated by leukapheresis of healthy donors, followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge. Monocytes were > 85% pure as determined by morphology and expression of CD14 antigen. Isolated monocytes were cultured in endotoxin-free RPMI 1640 medium supplemented with vitamins, antibiotics, pyruvate, nonessential amino acids, 5 x 10-8 M beta-mercaptoethanol, 2% human pooled AB-group serum and 100 ng/ml LPS on teflon foils for 4h hours.
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).


title: CTV1_PU1mut_2

tag: molecule subtype

value: transposed, nuclear DNA


title: Normal lung rep2

description: processed data file: genes_fpkm.txt

value: 8-10 weeks


title: Lung metastases rep1

description: processed data file: genes_fpkm.txt

value: Lung metastases

value: Wild type


title: Normal lung rep1

description: processed data file: genes_fpkm.txt


title: CTV1_PU1mut_1

value: T cell leukemia cell line


title: DC96h_FLAG-ChIP_donorM

description: Chromatin IP against FLAG-epitope

growth_protocol:
Peripheral blood monocytes were separated by leukapheresis of healthy donors followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge (Beckman Instruments) as previously described. Supernatants of monocyte cultures were routinely collected and analysed for the presence of interleukin 6, which was usually low, indicating that monocytes were not activated before or during elutriation. To generate immature dendritic cells, 1×10^6 monocytes/ml were cultured in RPMI 1640 medium (Gibco) supplemented with 10% fetal calf serum (FCS; Biowhittaker, Verviers, Belgium), 20 U/ml IL-4 (Promokine, Heidelberg, Germany) and 280 U/ml GM-CSF (Berlex, Seattle, USA).
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).

tag: donr id

value: donorM

value: MO-derived

value: primary monocyte-derived dendritic cells

value: FLAG (Sigma, #F3165)


title: KO-rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: FPKM

source_name: KO_Ovarian granulosa cells


title: MO4h_PU.1-ChIP_donorO

description: Chromatin IP against PU.1

growth_protocol:
Peripheral blood monocytes were separated by leukapheresis of healthy donors, followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge. Monocytes were > 85% pure as determined by morphology and expression of CD14 antigen. Isolated monocytes were cultured in endotoxin-free RPMI 1640 medium supplemented with vitamins, antibiotics, pyruvate, nonessential amino acids, 5 x 10-8 M beta-mercaptoethanol, 2% human pooled AB-group serum on teflon foils for 4 hours.
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).

value: donorO

tag: tissue/cell type

value: peripheral blood

value: PU.1 (Santa Cruz, #sc-352X)


title: CTV1_PU1_4


title: KO-rep1


title: MO18h_Input-ChIP_donorO

description: Chromatin input (control)

tag: cell subtype

value: primary monocytes


title: AM25-137BCD_S5_L008

first: Anqi

last: Ma

address: 1425 Madison Ave

department: Oncological Sciences

data_processing:
Trimmed low quality bases (PHRED < 10) and adapter sequences and then discarded short reads (length < 60nt) using bbduk tool (version 37.53)
Quantified the expression of transcripts using cleaned paired-end reads with Salmon tool (version 0.9.1) using human reference transcriptome from The Cancer Genome Atlas (TCGA) (GDC.h38 GENCODE v22)
Quantified the gene expression from the expression of transcripts using R tximport library (version 1.6.0) on R (version 3.4.3)
Pre-filtered genes to keep only genes that have at least 10 reads in total
Performed differential gene expression using R DESeq2 library (version 1.81.1)
Identified as differential expressed between two conditions when the p-value adjusted is at 5% and log2 fold change is more than 1
Performed gene set enrichment analysis that capture pathways perturbed towards both directions simultaneously using the 24,448 ranked genes identified in our dataset and annotated in ENSEMBL (version 94) against the KEGG pathways using R GAGE (version 2.28.2) and Pathview (version 1.18.2) libraries and the hallmarks gene set collection (MSigDB V6.2) using GSEA
Genome_build: hg38
transcriptome build: GDC.h38 GENCODE v22 (TCGA)
Supplementary_files_format_and_content: Salmon output (tab file)

molecule: polyA RNA

source_name: MDA-MD-468 breast cancer cell line

growth_protocol: 2E6 MDA-MB-468 cells were seeded in 10 cm dishes in duplicates and drugged at the indicated concentrations.

extract_protocol:
Cell samples were purified using Qiagen RNeasy Plus Mini Kit according to the protocols in RNeasy® Plus Mini Handbook published by Qiagen.
RNA-Seq libraries were constructed from the PolyA selected mRNA according to the protocol for the TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: We sequenced duplicated RNA samples (DMSO treated versus MS1943 treated [5 µM for 3 days])

value: Triple negative breast cancer cell line

tag: passage

tag: treated with

value: MS1943 degrader


title: AM25-137FGH_S7_L008


title: DC96h_PU.1-ChIP_donorM

description: Chromatin IP against PU.1


title: Normal lung rep3

description: processed data file: genes_fpkm.txt

tag: tissue

value: Normal lung


title: CTV1_PU1_3


title: CTV1_PU1_5


title: WT-rep2

source_name: WT_Ovarian granulosa cells

value: post natal day 24

value: ovary

value: Ovarian granulosa cells


title: AM25-137E_S6_L008

value: DMSO


title: DC96h_PU.1-ChIP_donorL

description: Chromatin IP against PU.1

value: donorL


title: AM25-137A_S9_L008


title: WT-rep1


title: CTV1_PU1_2

value: T cell leukemia cell line

value: transposed, nuclear DNA


title: con-rep1

value: con


title: CTV1_PU1_1


title: PRECap_PS1_3_A_FP+25_LY_UCAM-0

status: Public on Nov 16 2019

city: Oxford

first: Fabiola

last: Curion

state: Ox

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_3_A_FP+25_LY_UCAM-0_NFcapture, PRECap_PS1_3_A_FP+25_LY_UCAM-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_3_A_FP+25_LY_UCAM-0

data_processing:
basecalls using Illumina bcl2Fastq Version 2.20.0
fastq trimming using Skewer Version 0.1.125
alignment using Hisat2 Version 2.1.0
removal of PCR duplicates with Picard Version 2.0.1
transcriptomic assembly using StringTie Version 1.3.4
read quality and coverage check with Samtools (1.4.1) and Bedtools (2.27.0)
assembly inspection with GFFcompare Version 0.10.4
read alignment quatification into gene counts with featureCount Version 1.6.2
Genome_build: hg38
Supplementary_files_format_and_content: gene counts tables generated using featureCounts

source_name: Dermal fibroblasts differentiated into iPS cells

extract_protocol:
RNeasy Mini Kits (QIAGEN)
polyA based Rnaseq

tag: condition

tag: celline

tag: days of culture

tag: type of bulk data

value: Multicentre Bulk

tag: capture panel

value: PreCapture data NFCapture 850NG ,PreCapture data TFCapture 850NG


title: PRECap_PS1_3_A_FP+55_LY_JANS-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_3_A_FP+55_LY_JANS-0_NFcapture, PRECap_PS1_3_A_FP+55_LY_JANS-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_3_A_FP+55_LY_JANS-0


title: PRECap_PS1_3_A_FP+55_LY_UCAM-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_3_A_FP+55_LY_UCAM-0_NFcapture, PRECap_PS1_3_A_FP+55_LY_UCAM-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_3_A_FP+55_LY_UCAM-0


title: PRECap_PS1_3_A_FP+55_LY_ABBV-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_3_A_FP+55_LY_ABBV-0_NFcapture, PRECap_PS1_3_A_FP+55_LY_ABBV-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_3_A_FP+55_LY_ABBV-0


title: PRECap_PS1_3_A_FP+25_LY_UOXC-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_3_A_FP+25_LY_UOXC-0_NFcapture, PRECap_PS1_3_A_FP+25_LY_UOXC-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_3_A_FP+25_LY_UOXC-0


title: PRECap_PS1_3_A_FP+55_LY_UOXC-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_3_A_FP+55_LY_UOXC-0_NFcapture, PRECap_PS1_3_A_FP+55_LY_UOXC-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_3_A_FP+55_LY_UOXC-0


title: PRECap_PS1_3_A_FP+25_LY_ABBV-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_3_A_FP+25_LY_ABBV-0_NFcapture, PRECap_PS1_3_A_FP+25_LY_ABBV-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_3_A_FP+25_LY_ABBV-0


title: PRECap_PS1_2_A_FP+55_LY_UOXC-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_2_A_FP+55_LY_UOXC-0_NFcapture, PRECap_PS1_2_A_FP+55_LY_UOXC-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_2_A_FP+55_LY_UOXC-0


title: PRECap_PS1_2_A_FP+55_LY_JANS-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_2_A_FP+55_LY_JANS-0_NFcapture, PRECap_PS1_2_A_FP+55_LY_JANS-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_2_A_FP+55_LY_JANS-0


title: PRECap_PS1_2_A_FP+55_LY_ABBV-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_2_A_FP+55_LY_ABBV-0_NFcapture, PRECap_PS1_2_A_FP+55_LY_ABBV-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_2_A_FP+55_LY_ABBV-0


title: DC96h_FLAG-ChIP_donorL

description: Chromatin IP against FLAG-epitope

value: MO-derived

value: primary monocyte-derived dendritic cells

value: FLAG (Sigma, #F3165)


title: PRECap_PS1_2_A_FP+25_LY_UOXZ-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_2_A_FP+25_LY_UOXZ-0_NFcapture, PRECap_PS1_2_A_FP+25_LY_UOXZ-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_2_A_FP+25_LY_UOXZ-0


title: PRECap_PS1_2_A_FP+55_LY_UCAM-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_2_A_FP+55_LY_UCAM-0_NFcapture, PRECap_PS1_2_A_FP+55_LY_UCAM-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_2_A_FP+55_LY_UCAM-0


title: PRECap_PS1_2_A_FP+25_LY_JANS-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_2_A_FP+25_LY_JANS-0_NFcapture, PRECap_PS1_2_A_FP+25_LY_JANS-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_2_A_FP+25_LY_JANS-0


title: PRECap_PS1_2_A_FP+25_LY_UOXC-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_2_A_FP+25_LY_UOXC-0_NFcapture, PRECap_PS1_2_A_FP+25_LY_UOXC-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_2_A_FP+25_LY_UOXC-0


title: PRECap_PS1_2_A_FP+25_LY_UCAM-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_2_A_FP+25_LY_UCAM-0_NFcapture, PRECap_PS1_2_A_FP+25_LY_UCAM-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_2_A_FP+25_LY_UCAM-0


title: PRECap_PS1_2_A_FP+25_LY_ABBV-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_2_A_FP+25_LY_ABBV-0_NFcapture, PRECap_PS1_2_A_FP+25_LY_ABBV-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_2_A_FP+25_LY_ABBV-0


title: PRECap_PS1_1_A_FP+55_LY_UOXZ-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_1_A_FP+55_LY_UOXZ-0_NFcapture, PRECap_PS1_1_A_FP+55_LY_UOXZ-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_1_A_FP+55_LY_UOXZ-0


title: PRECap_PS1_1_A_FP+55_LY_UCAM-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_1_A_FP+55_LY_UCAM-0_NFcapture, PRECap_PS1_1_A_FP+55_LY_UCAM-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_1_A_FP+55_LY_UCAM-0


title: MO_PU.1-ChIP_donorO

description: Chromatin IP against PU.1

growth_protocol:
Peripheral blood monocytes were separated by leukapheresis of healthy donors, followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge (Beckman, München, Germany).
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).

value: donorO

value: peripheral blood

value: primary monocytes

value: PU.1 (Santa Cruz, #sc-352X)


title: PRECap_PS1_1_A_FP+55_LY_ABBV-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_1_A_FP+55_LY_ABBV-0_NFcapture, PRECap_PS1_1_A_FP+55_LY_ABBV-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_1_A_FP+55_LY_ABBV-0


title: PRECap_PS1_1_A_FP+55_LY_JANS-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_1_A_FP+55_LY_JANS-0_NFcapture, PRECap_PS1_1_A_FP+55_LY_JANS-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_1_A_FP+55_LY_JANS-0


title: PRECap_PS1_1_A_FP+25_LY_UOXC-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_1_A_FP+25_LY_UOXC-0_NFcapture, PRECap_PS1_1_A_FP+25_LY_UOXC-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_1_A_FP+25_LY_UOXC-0


title: PRECap_PS1_1_A_FP+25_LY_UOXZ-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_1_A_FP+25_LY_UOXZ-0_NFcapture, PRECap_PS1_1_A_FP+25_LY_UOXZ-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_1_A_FP+25_LY_UOXZ-0


title: PRECap_PS1_1_A_FP+25_LY_UCAM-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_1_A_FP+25_LY_UCAM-0_NFcapture, PRECap_PS1_1_A_FP+25_LY_UCAM-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_1_A_FP+25_LY_UCAM-0


title: PRECap_PS1_3_A_FP+25_LY_JANS-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_3_A_FP+25_LY_JANS-0_NFcapture, PRECap_PS1_3_A_FP+25_LY_JANS-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_3_A_FP+25_LY_JANS-0


title: PRECap_PS1_2_A_FP+55_LY_UOXZ-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_2_A_FP+55_LY_UOXZ-0_NFcapture, PRECap_PS1_2_A_FP+55_LY_UOXZ-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_2_A_FP+55_LY_UOXZ-0


title: PRECap_PS1_1_A_FP+25_LY_JANS-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_1_A_FP+25_LY_JANS-0_NFcapture, PRECap_PS1_1_A_FP+25_LY_JANS-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_1_A_FP+25_LY_JANS-0


title: PRECap_PS1_1_A_FP+25_LY_ABBV-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_1_A_FP+25_LY_ABBV-0_NFcapture, PRECap_PS1_1_A_FP+25_LY_ABBV-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_1_A_FP+25_LY_ABBV-0


title: PRECap_CON_3_A_FP+55_LY_UOXZ-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_3_A_FP+55_LY_UOXZ-0_NFcapture, PRECap_CON_3_A_FP+55_LY_UOXZ-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_3_A_FP+55_LY_UOXZ-0

value: CON

value: line SB-AD3-1


title: PRECap_CON_3_A_FP+55_LY_UOXC-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_3_A_FP+55_LY_UOXC-0_NFcapture, PRECap_CON_3_A_FP+55_LY_UOXC-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_3_A_FP+55_LY_UOXC-0


title: PRECap_CON_3_A_FP+55_LY_ABBV-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_3_A_FP+55_LY_ABBV-0_NFcapture, PRECap_CON_3_A_FP+55_LY_ABBV-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_3_A_FP+55_LY_ABBV-0


title: PRECap_CON_3_A_FP+55_LY_JANS-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_3_A_FP+55_LY_JANS-0_NFcapture, PRECap_CON_3_A_FP+55_LY_JANS-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_3_A_FP+55_LY_JANS-0


title: PRECap_CON_3_A_FP+55_LY_UCAM-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_3_A_FP+55_LY_UCAM-0_NFcapture, PRECap_CON_3_A_FP+55_LY_UCAM-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_3_A_FP+55_LY_UCAM-0


title: PRECap_CON_3_A_FP+25_LY_UOXC-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_3_A_FP+25_LY_UOXC-0_NFcapture, PRECap_CON_3_A_FP+25_LY_UOXC-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_3_A_FP+25_LY_UOXC-0


title: PRECap_CON_3_A_FP+25_LY_UCAM-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_3_A_FP+25_LY_UCAM-0_NFcapture, PRECap_CON_3_A_FP+25_LY_UCAM-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_3_A_FP+25_LY_UCAM-0


title: PRECap_CON_2_A_FP+55_LY_UOXZ-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_2_A_FP+55_LY_UOXZ-0_NFcapture, PRECap_CON_2_A_FP+55_LY_UOXZ-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_2_A_FP+55_LY_UOXZ-0


title: PRECap_CON_3_A_FP+25_LY_ABBV-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_3_A_FP+25_LY_ABBV-0_NFcapture, PRECap_CON_3_A_FP+25_LY_ABBV-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_3_A_FP+25_LY_ABBV-0


title: PRECap_CON_2_A_FP+55_LY_UOXC-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_2_A_FP+55_LY_UOXC-0_NFcapture, PRECap_CON_2_A_FP+55_LY_UOXC-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_2_A_FP+55_LY_UOXC-0


title: PRECap_CON_3_A_FP+25_LY_JANS-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_3_A_FP+25_LY_JANS-0_NFcapture, PRECap_CON_3_A_FP+25_LY_JANS-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_3_A_FP+25_LY_JANS-0


title: PRECap_PS1_1_A_FP+55_LY_UOXC-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_PS1_1_A_FP+55_LY_UOXC-0_NFcapture, PRECap_PS1_1_A_FP+55_LY_UOXC-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
PS1_1_A_FP+55_LY_UOXC-0


title: PRECap_CON_2_A_FP+25_LY_UOXZ-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_2_A_FP+25_LY_UOXZ-0_NFcapture, PRECap_CON_2_A_FP+25_LY_UOXZ-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_2_A_FP+25_LY_UOXZ-0


title: PRECap_CON_2_A_FP+25_LY_UOXC-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_2_A_FP+25_LY_UOXC-0_NFcapture, PRECap_CON_2_A_FP+25_LY_UOXC-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_2_A_FP+25_LY_UOXC-0


title: PRECap_CON_2_A_FP+55_LY_JANS-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_2_A_FP+55_LY_JANS-0_NFcapture, PRECap_CON_2_A_FP+55_LY_JANS-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_2_A_FP+55_LY_JANS-0


title: PRECap_CON_2_A_FP+25_LY_JANS-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_2_A_FP+25_LY_JANS-0_NFcapture, PRECap_CON_2_A_FP+25_LY_JANS-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_2_A_FP+25_LY_JANS-0


title: PRECap_CON_2_A_FP+55_LY_ABBV-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_2_A_FP+55_LY_ABBV-0_NFcapture, PRECap_CON_2_A_FP+55_LY_ABBV-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_2_A_FP+55_LY_ABBV-0


title: PRECap_CON_2_A_FP+25_LY_UCAM-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_2_A_FP+25_LY_UCAM-0_NFcapture, PRECap_CON_2_A_FP+25_LY_UCAM-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_2_A_FP+25_LY_UCAM-0


title: PRECap_CON_2_A_FP+25_LY_ABBV-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_2_A_FP+25_LY_ABBV-0_NFcapture, PRECap_CON_2_A_FP+25_LY_ABBV-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_2_A_FP+25_LY_ABBV-0


title: PRECap_CON_1_A_FP+55_LY_UOXC-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_1_A_FP+55_LY_UOXC-0_NFcapture, PRECap_CON_1_A_FP+55_LY_UOXC-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_1_A_FP+55_LY_UOXC-0


title: PRECap_CON_1_A_FP+55_LY_JANS-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_1_A_FP+55_LY_JANS-0_NFcapture, PRECap_CON_1_A_FP+55_LY_JANS-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_1_A_FP+55_LY_JANS-0


title: PRECap_CON_1_A_FP+55_LY_ABBV-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_1_A_FP+55_LY_ABBV-0_NFcapture, PRECap_CON_1_A_FP+55_LY_ABBV-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_1_A_FP+55_LY_ABBV-0


title: PRECap_CON_1_A_FP+55_LY_UOXZ-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_1_A_FP+55_LY_UOXZ-0_NFcapture, PRECap_CON_1_A_FP+55_LY_UOXZ-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_1_A_FP+55_LY_UOXZ-0


title: PRECap_CON_1_A_FP+25_LY_UOXZ-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_1_A_FP+25_LY_UOXZ-0_NFcapture, PRECap_CON_1_A_FP+25_LY_UOXZ-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_1_A_FP+25_LY_UOXZ-0


title: PRECap_CON_1_A_FP+25_LY_UOXC-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_1_A_FP+25_LY_UOXC-0_NFcapture, PRECap_CON_1_A_FP+25_LY_UOXC-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_1_A_FP+25_LY_UOXC-0


title: PRECap_CON_3_A_FP+25_LY_UOXZ-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_3_A_FP+25_LY_UOXZ-0_NFcapture, PRECap_CON_3_A_FP+25_LY_UOXZ-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_3_A_FP+25_LY_UOXZ-0


title: PRECap_CON_1_A_FP+25_LY_UCAM-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_1_A_FP+25_LY_UCAM-0_NFcapture, PRECap_CON_1_A_FP+25_LY_UCAM-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_1_A_FP+25_LY_UCAM-0


title: PRECap_CON_1_A_FP+25_LY_JANS-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_1_A_FP+25_LY_JANS-0_NFcapture, PRECap_CON_1_A_FP+25_LY_JANS-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_1_A_FP+25_LY_JANS-0


title: PRECap_WTCHG_264983_228208_TFCapture

description:
Pre capture data for the Minibulk TF Capture panel 850ng and 150ng
raw.counts.MINIBULKS.TF.150ng.txt, raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_264983_228208

value: Minibulk

value: PreCapture data TFCapture 850NG, PreCapture data TFCapture 150NG


title: PRECap_WTCHG_264983_256208_TFCapture

description:
Pre capture data for the Minibulk TF Capture panel 850ng and 150ng
raw.counts.MINIBULKS.TF.150ng.txt, raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_264983_256208


title: PRECap_CON_1_A_FP+25_LY_ABBV-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_1_A_FP+25_LY_ABBV-0_NFcapture, PRECap_CON_1_A_FP+25_LY_ABBV-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_1_A_FP+25_LY_ABBV-0


title: PRECap_WTCHG_264983_228232_TFCapture

description:
Pre capture data for the Minibulk TF Capture panel 850ng and 150ng
raw.counts.MINIBULKS.TF.150ng.txt, raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_264983_228232


title: PRECap_WTCHG_264983_255208_TFCapture

description:
Pre capture data for the Minibulk TF Capture panel 850ng and 150ng
raw.counts.MINIBULKS.TF.150ng.txt, raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_264983_255208


title: PRECap_WTCHG_264983_227232_TFCapture

description:
Pre capture data for the Minibulk TF Capture panel 850ng and 150ng
raw.counts.MINIBULKS.TF.150ng.txt, raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_264983_227232


title: PRECap_WTCHG_255094_256280_NFCapture

description:
Pre capture data for the Minibulk NF Capture panel 850ng
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_255094_256280

value: PreCapture data NFCapture 850NG


title: PRECap_WTCHG_264983_227208_TFCapture

description:
Pre capture data for the Minibulk TF Capture panel 850ng and 150ng
raw.counts.MINIBULKS.TF.150ng.txt, raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_264983_227208


title: PRECap_WTCHG_255094_256256_NFCapture

description:
Pre capture data for the Minibulk NF Capture panel 850ng
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_255094_256256


title: PRECap_WTCHG_255094_255280_NFCapture

description:
Pre capture data for the Minibulk NF Capture panel 850ng
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_255094_255280


title: PRECap_WTCHG_255094_255256_NFCapture

description:
Pre capture data for the Minibulk NF Capture panel 850ng
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_255094_255256


title: PRECap_WTCHG_255094_228280_NFCapture

description:
Pre capture data for the Minibulk NF Capture panel 850ng
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_255094_228280


title: PRECap_WTCHG_255094_228256_NFCapture

description:
Pre capture data for the Minibulk NF Capture panel 850ng
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_255094_228256


title: PRECap_CON_1_A_FP+55_LY_UCAM-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_1_A_FP+55_LY_UCAM-0_NFcapture, PRECap_CON_1_A_FP+55_LY_UCAM-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_1_A_FP+55_LY_UCAM-0


title: PRECap_WTCHG_255094_227256_NFCapture

description:
Pre capture data for the Minibulk NF Capture panel 850ng
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_255094_227256


title: POSTCap_WTCHG_473874_256232_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.150ng.txt
WTCHG_473874_256232

extract_protocol:
RNeasy Mini Kits (QIAGEN)
targeted enrichment with Roche NimbleGen SeqCap

value: TFCapture 150NG


title: POSTCap_WTCHG_473874_255208_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.150ng.txt
WTCHG_473874_255208


title: POSTCap_WTCHG_473874_256208_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.150ng.txt
WTCHG_473874_256208


title: POSTCap_WTCHG_473874_227232_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.150ng.txt
WTCHG_473874_227232


title: PRECap_WTCHG_264983_256232_TFCapture

description:
Pre capture data for the Minibulk TF Capture panel 850ng and 150ng
raw.counts.MINIBULKS.TF.150ng.txt, raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_264983_256232


title: POSTCap_WTCHG_473873_256208_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_473873_256208

value: TFCapture 850NG


title: POSTCap_WTCHG_473873_255232_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_473873_255232


title: POSTCap_WTCHG_473874_227208_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.150ng.txt
WTCHG_473874_227208


title: PRECap_WTCHG_264983_255232_TFCapture

description:
Pre capture data for the Minibulk TF Capture panel 850ng and 150ng
raw.counts.MINIBULKS.TF.150ng.txt, raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_264983_255232


title: POSTCap_WTCHG_473873_256232_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_473873_256232


title: POSTCap_WTCHG_473873_228232_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_473873_228232


title: POSTCap_WTCHG_473873_228208_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_473873_228208


title: POSTCap_WTCHG_473873_227208_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_473873_227208


title: PRECap_CON_2_A_FP+55_LY_UCAM-0

description:
Pre capture data for the Multicentre Bulk NF Capture panel and TF capture panel 850ng
PRECap_CON_2_A_FP+55_LY_UCAM-0_NFcapture, PRECap_CON_2_A_FP+55_LY_UCAM-0_TFcapture
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt,raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
CON_2_A_FP+55_LY_UCAM-0


title: POSTCap_WTCHG_422059_256280_NFcapture

description:
PostCapture data
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_422059_256280

value: NFCapture 850NG


title: POSTCap_WTCHG_422059_256256_NFcapture

description:
PostCapture data
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_422059_256256


title: POSTCap_WTCHG_473874_228208_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.150ng.txt
WTCHG_473874_228208


title: POSTCap_WTCHG_422059_228256_NFcapture

description:
PostCapture data
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_422059_228256


title: PRECap_WTCHG_255094_227280_NFCapture

description:
Pre capture data for the Minibulk NF Capture panel 850ng
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_255094_227280


title: POSTCap_WTCHG_473874_255232_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.150ng.txt
WTCHG_473874_255232


title: POSTCap_WTCHG_422059_228280_NFcapture

description:
PostCapture data
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_422059_228280


title: POSTCap_PS1_1_A_FP+55_LY_UOXZ-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_285

value: Multicentre Bulk


title: POSTCap_WTCHG_473874_228232_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.150ng.txt
WTCHG_473874_228232


title: POSTCap_WTCHG_422059_227280_NFcapture

description:
PostCapture data
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_422059_227280


title: POSTCap_WTCHG_422059_227256_NFcapture

description:
PostCapture data
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_422059_227256


title: POSTCap_PS1_2_A_FP+55_LY_UOXZ-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_286


title: POSTCap_CON_2_A_FP+55_LY_UOXZ-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_283


title: POSTCap_CON_1_A_FP+55_LY_UOXZ-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_282


title: POSTCap_PS1_2_A_FP+25_LY_UOXZ-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_281


title: POSTCap_PS1_1_A_FP+25_LY_UOXZ-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_280


title: POSTCap_WTCHG_473873_227232_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_473873_227232


title: POSTCap_CON_2_A_FP+25_LY_UOXZ-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_278


title: POSTCap_WTCHG_422059_255256_NFcapture

description:
PostCapture data
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_422059_255256


title: POSTCap_PS1_1_A_FP+55_LY_UOXC-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_274


title: POSTCap_CON_1_A_FP+25_LY_UOXZ-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_277


title: POSTCap_CON_1_A_FP+55_LY_UOXC-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_271


title: POSTCap_PS1_2_A_FP+55_LY_UOXC-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_275


title: POSTCap_WTCHG_473873_255208_TFcapture

description:
PostCapture data
raw.counts.MINIBULKS.TF.850ng.txt
WTCHG_473873_255208


title: POSTCap_PS1_2_A_FP+25_LY_UOXC-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_269


title: POSTCap_PS1_3_A_FP+25_LY_UOXC-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_270


title: POSTCap_PS1_3_A_FP+55_LY_UOXC-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_276


title: POSTCap_CON_3_A_FP+55_LY_UOXC-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_273


title: POSTCap_WTCHG_422059_255280_NFcapture

description:
PostCapture data
raw.counts.MINIBULKS.NF.850ng.txt
WTCHG_422059_255280


title: POSTCap_CON_2_A_FP+25_LY_UOXC-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_266


title: POSTCap_PS1_1_A_FP+25_LY_UOXC-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_268


title: POSTCap_CON_1_A_FP+25_LY_UOXC-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_265


title: POSTCap_PS1_2_A_FP+55_LY_UCAM-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_263


title: POSTCap_PS1_1_A_FP+55_LY_UCAM-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_262


title: POSTCap_CON_3_A_FP+25_LY_UOXC-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_267


title: POSTCap_CON_3_A_FP+55_LY_UOXZ-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_284


title: POSTCap_CON_1_A_FP+55_LY_UCAM-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_259


title: POSTCap_CON_3_A_FP+55_LY_UCAM-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_261


title: POSTCap_PS1_1_A_FP+25_LY_UCAM-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_256


title: POSTCap_PS1_2_A_FP+25_LY_UCAM-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_257


title: POSTCap_PS1_3_A_FP+55_LY_UCAM-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_264


title: POSTCap_PS1_3_A_FP+25_LY_UCAM-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_258


title: POSTCap_CON_3_A_FP+25_LY_UCAM-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_255


title: POSTCap_CON_2_A_FP+25_LY_UCAM-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_254


title: POSTCap_CON_2_A_FP+55_LY_UOXC-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_272


title: POSTCap_PS1_3_A_FP+55_LY_JANS-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_252


title: POSTCap_PS1_2_A_FP+55_LY_JANS-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_251


title: POSTCap_PS1_1_A_FP+55_LY_JANS-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_250


title: POSTCap_CON_1_A_FP+25_LY_UCAM-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_253


title: POSTCap_CON_1_A_FP+55_LY_JANS-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_247


title: POSTCap_PS1_1_A_FP+25_LY_JANS-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_244


title: POSTCap_PS1_3_A_FP+25_LY_JANS-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_246


title: POSTCap_CON_3_A_FP+55_LY_JANS-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_249


title: POSTCap_CON_3_A_FP+25_LY_JANS-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_243


title: POSTCap_PS1_1_A_FP+55_LY_ABBV-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_238


title: POSTCap_PS1_3_A_FP+55_LY_ABBV-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_240


title: POSTCap_CON_1_A_FP+25_LY_JANS-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_241


title: POSTCap_CON_2_A_FP+55_LY_JANS-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_248


title: POSTCap_PS1_2_A_FP+25_LY_JANS-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_245


title: POSTCap_CON_2_A_FP+25_LY_JANS-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_242


title: POSTCap_PS1_2_A_FP+55_LY_ABBV-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_239


title: POSTCap_CON_1_A_FP+55_LY_ABBV-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_235


title: POSTCap_CON_2_A_FP+55_LY_ABBV-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_236


title: POSTCap_CON_2_A_FP+55_LY_UCAM-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_260


title: POSTCap_CON_3_A_FP+55_LY_ABBV-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_237


title: POSTCap_CON_3_A_FP+25_LY_ABBV-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_231


title: POSTCap_PS1_2_A_FP+25_LY_ABBV-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_233


title: POSTCap_PS1_1_A_FP+55_LY_UOXZ-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_285


title: POSTCap_PS1_3_A_FP+25_LY_ABBV-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_234


title: POSTCap_PS1_1_A_FP+25_LY_ABBV-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_232


title: POSTCap_CON_2_A_FP+25_LY_ABBV-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_230


title: POSTCap_CON_1_A_FP+25_LY_ABBV-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_229


title: POSTCap_CON_1_A_FP+55_LY_UOXZ-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_282


title: POSTCap_CON_3_A_FP+55_LY_UOXZ-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_284


title: POSTCap_PS1_2_A_FP+55_LY_UOXZ-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_286


title: POSTCap_PS1_2_A_FP+25_LY_UOXZ-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_281


title: POSTCap_CON_1_A_FP+25_LY_UOXZ-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_277


title: POSTCap_CON_2_A_FP+25_LY_UOXZ-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_278


title: POSTCap_CON_3_A_FP+25_LY_UOXZ-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_279


title: POSTCap_PS1_1_A_FP+25_LY_UOXZ-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_280


title: POSTCap_PS1_1_A_FP+55_LY_UOXC-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_274


title: POSTCap_PS1_2_A_FP+55_LY_UOXC-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_275


title: POSTCap_PS1_3_A_FP+55_LY_UOXC-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_276


title: POSTCap_PS1_1_A_FP+25_LY_UOXC-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_268


title: POSTCap_CON_3_A_FP+55_LY_UOXC-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_273


title: POSTCap_PS1_3_A_FP+25_LY_UOXC-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_270


title: POSTCap_CON_3_A_FP+25_LY_UOXZ-0_NFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.NF.850ng.txt
WTCHG_476962_279


title: POSTCap_PS1_2_A_FP+25_LY_UOXC-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_269


title: POSTCap_CON_2_A_FP+25_LY_UOXC-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_266


title: POSTCap_CON_1_A_FP+25_LY_UOXC-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_265


title: POSTCap_CON_2_A_FP+55_LY_UOXZ-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_283


title: POSTCap_CON_2_A_FP+55_LY_UOXC-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_272


title: POSTCap_CON_3_A_FP+25_LY_UOXC-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_267


title: POSTCap_PS1_2_A_FP+55_LY_UCAM-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_263


title: POSTCap_PS1_1_A_FP+55_LY_UCAM-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_262


title: POSTCap_PS1_3_A_FP+55_LY_UCAM-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_264


title: POSTCap_CON_1_A_FP+55_LY_UOXC-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_271


title: POSTCap_CON_2_A_FP+55_LY_UCAM-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_260


title: POSTCap_CON_3_A_FP+55_LY_UCAM-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_261


title: POSTCap_CON_3_A_FP+25_LY_UCAM-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_255


title: POSTCap_CON_1_A_FP+55_LY_UCAM-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_259


title: POSTCap_CON_1_A_FP+25_LY_UCAM-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_253


title: POSTCap_CON_2_A_FP+25_LY_UCAM-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_254


title: POSTCap_PS1_2_A_FP+55_LY_JANS-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_251


title: POSTCap_PS1_3_A_FP+55_LY_JANS-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_252


title: POSTCap_PS1_1_A_FP+55_LY_JANS-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_250


title: POSTCap_CON_3_A_FP+55_LY_JANS-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_249


title: POSTCap_PS1_3_A_FP+25_LY_JANS-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_246


title: POSTCap_PS1_3_A_FP+25_LY_UCAM-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_258


title: POSTCap_CON_2_A_FP+25_LY_JANS-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_242


title: POSTCap_PS1_3_A_FP+55_LY_ABBV-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_240


title: POSTCap_PS1_2_A_FP+25_LY_JANS-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_245


title: POSTCap_CON_3_A_FP+25_LY_JANS-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_243


title: POSTCap_CON_3_A_FP+55_LY_ABBV-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_237


title: POSTCap_CON_2_A_FP+55_LY_ABBV-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_236


title: POSTCap_PS1_1_A_FP+55_LY_ABBV-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_238


title: POSTCap_CON_2_A_FP+55_LY_JANS-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_248


title: POSTCap_CON_1_A_FP+55_LY_JANS-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_247


title: POSTCap_CON_1_A_FP+25_LY_JANS-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_241


title: POSTCap_PS1_2_A_FP+25_LY_ABBV-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_233


title: POSTCap_CON_1_A_FP+55_LY_ABBV-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_235


title: POSTCap_PS1_2_A_FP+55_LY_ABBV-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_239


title: POSTCap_PS1_1_A_FP+25_LY_UCAM-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_256


title: POSTCap_CON_3_A_FP+25_LY_ABBV-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_231


title: POSTCap_PS1_1_A_FP+25_LY_ABBV-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_232


title: POSTCap_PS1_2_A_FP+25_LY_UCAM-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_257


title: POSTCap_PS1_3_A_FP+25_LY_ABBV-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_234


title: POSTCap_CON_2_A_FP+25_LY_ABBV-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_230


title: POSTCap_CON_1_A_FP+25_LY_ABBV-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_229


title: SCbeta_H3K4me1_rep1

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: hPSC_DE_PP1_PP2_EN_Scbeta_PH_Alpha_Beta.H3K27ac_enhancer_domains.merged.bed

data_processing:
Sequencing reads were mapped to the human hg19 reference genome assembly using bowtie2 (Langmead and Salzberg, 2012) with default parameters. Peak calling was performed using MACS2 (Zhang et al., 2008) with default parameters and “--broad --qvalue 0.01” to composite broad regions of read enrichment over background with a minimum FDR q-value cutoff of 0.01, using whole-cell extract from each stage as the background control. H3K4me1 and H3K27ac peaks across all cell types were concatenated and merged whenever overlapping by BEDTools (Quinlan and Hall, 2010) to obtain a unified catalog of H3K27ac/H3K4me1 regions (Figure S4) .
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited bed  file containing enhancer domain coordinates

source_name: HUES 8 hESC line

growth_protocol: Undifferentiated stem cells were maintained as aggregates in supplemented mTeSR1 medium (StemCell Technologies) using spinner flasks (Corning) set at a 70rpm rotation rate in a 37ºC 5% CO2 incubator. Directed hPSC differentiation into islet cells was conducted as described in the methods of (Alvarez-Dominguez et al. 2019).

extract_protocol:
FACS-purified fixed cells (typically ~1million) were pelleted and flash-frozen. ChIP-seq was conducted as described in (Gifford et al., 2013) with minor modifications. Briefly, cell pellets were thawed on ice for 30min, incubated in lysis buffer (0.5% NP-40 +85mM KCl +20mM Tris-HCl pH8.0 +protease inhibitor) for 10min on ice, and nuclei were pelleted and incubated in lysis buffer (1% NP-40 +0.5% sodium deoxycholate +0.1% SDS +10mM Tris-HCl pH7.5 +protease inhibitor) for 10min on ice. Chromatin was then sheared with a Branson Sonifier (model S-450D) at 4ºC and incubated with 1µg/million cells H3K27Ac (Active Motif; 39133) or H3K4me1 (Millipore, 17-614) antibody overnight at 4ºC. Next, antibody-protein complexes were isolated by incubation with Protein A/G beads (Life Technologies; 100-02D/100-07D) for 2h at 4ºC. Samples were then sequentially washed twice with low-salt buffer (0.1% SDS +1% Triton X-100 +2mM EDTA +20mM Tris-HCl pH8.1 +150mM NaCl), twice with high-salt buffer (0.1% SDS +1% Triton X-100 +2mM EDTA +20mM Tris), twice with LiCl buffer (0.25M LiCl +1% NP-40 +1% deoxycholate +1mM EDTA +10mM Tris-HCl pH8.1), twice with TE (10mM Tris-HCl pH8.0 +1mM EDTA), and finally eluted in freshly-prepared elution buffer (1% SDS +0.1M NaHCO3) at 65ºC for 30min. Eluates were then treated with reverse crosslinking salt mixture (250mM Tris-HCl pH6.5 +62.5mM EDTA pH8.0 +1.25M NaCl +5mg/ml Proteinase K + 62.5ng/µl RNase A) overnight at 65ºC
DNA was purified using AMPure XP magnetic beads (Beckman Coulter), and sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs; E7103), pooled, and sequenced on a HiSeq 2500 instrument (Illumina).

tag: cell line

value: HUES 8 hESC line

value: hPSC-derived beta cell

tag: Stage

value: Stage 6 day 8

value: H3K4me1 (Millipore:17-614)


title: EN_H3K4me1_rep1

tag: cell type

value: hPSC-derived endocrine progenitor

value: Stage 5 day 3


title: PH_H3K4me1_rep1

value: hPSC-derived poly-hormonal cell

tag: chip antibody


title: Beta_H3K27ac_rep1

description:
Beta_SE.byH3K27ac.bed
Beta_TE.byH3K27ac.bed
hPSC_DE_PP1_PP2_EN_Scbeta_PH_Alpha_Beta.H3K27ac_enhancer_domains.merged.bed

value: Primary adult beta cell

value: H3K27ac (Active Motif:39133)


title: Alpha_H3K27ac_rep1

description:
Alpha_SE.byH3K27ac.bed
Alpha_TE.byH3K27ac.bed
hPSC_DE_PP1_PP2_EN_Scbeta_PH_Alpha_Beta.H3K27ac_enhancer_domains.merged.bed

value: Primary adult alpha cell


title: PH_H3K27ac_rep2

description:
PH_SE.byH3K27ac.bed
PH_TE.byH3K27ac.bed
hPSC_DE_PP1_PP2_EN_Scbeta_PH_Alpha_Beta.H3K27ac_enhancer_domains.merged.bed


title: PH_H3K27ac_rep1


title: SCbeta_WCE

description:
SCbeta_SE.byH3K27ac.bed
SCbeta_TE.byH3K27ac.bed
hPSC_DE_PP1_PP2_EN_Scbeta_PH_Alpha_Beta.H3K27ac_enhancer_domains.merged.bed


title: SCbeta_H3K27ac_rep1


title: PP2_H3K27ac_rep1

description:
PP2_SE.byH3K27ac.bed
PP2_TE.byH3K27ac.bed
hPSC_DE_PP1_PP2_EN_Scbeta_PH_Alpha_Beta.H3K27ac_enhancer_domains.merged.bed

value: hPSC-derived pancreatic progenitor 2

value: Stage 4 day 5


title: EN_H3K27ac_rep1

description:
EN_SE.byH3K27ac.bed
EN_TE.byH3K27ac.bed
hPSC_DE_PP1_PP2_EN_Scbeta_PH_Alpha_Beta.H3K27ac_enhancer_domains.merged.bed


title: PP1_WCE

description:
PP1_SE.byH3K27ac.bed
PP1_TE.byH3K27ac.bed
hPSC_DE_PP1_PP2_EN_Scbeta_PH_Alpha_Beta.H3K27ac_enhancer_domains.merged.bed

value: hPSC-derived pancreatic progenitor 1

value: Stage 3 day 2


title: SCbeta_H3K27ac_rep2


title: POSTCap_PS1_1_A_FP+25_LY_JANS-0_TFcapture

description:
PostCapture data
raw.counts.MULTICENTRE.BULKS.TF.850ng.txt
WTCHG_476961_244

value: TFCapture 850NG


title: PP2_WCE


title: EN_WCE


title: PP1_H3K27ac_rep1


title: DE_H3K27ac_rep2

description:
DE_SE.byH3K27ac.bed
DE_TE.byH3K27ac.bed
hPSC_DE_PP1_PP2_EN_Scbeta_PH_Alpha_Beta.H3K27ac_enhancer_domains.merged.bed

value: hPSC-derived definitive endoderm

value: Stage 1 day 3


title: DE_H3K27ac_rep1

value: HUES 8 hESC line


title: DE_WCE


title: EN_H3K27ac_rep2


title: Beta_ATAC_rep1

data_processing:
Sequencing reads were mapped to the human hg19 reference genome assembly using bowtie2 (Langmead and Salzberg, 2012) with default parameters. Peak calling was performed using MACS2 (Zhang et al., 2008) with default parameters, “--nomodel --shift 37 --extsize 73” to bypass building a ChIP-based shifting model and instead shift read 5’-ends and extend in the 5'->3' direction by a half-nucleosome size (73bp), and  “--broad --qvalue 0.01” to composite broad regions of read enrichment with a minimum FDR q-value cutoff of 0.01.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file with peak coordinates

source_name: Primary human adult islets

extract_protocol:
Live cells (typically ~50,000) were pelleted and tagmentation was performed at 37ºC for 30min as described in (Buenrostro et al., 2013). Briefly, cell pellets were resuspended in buffer containing Tn5 Transposase (Nextera DNA Sample Preparation kit; Illumina), incubated at 37ºC for 30min, and DNA was isolated using the MinElute PCR purification kit (Qiagen).
Tagmented DNA was PCR-amplified for 10 cycles and purified using AMPure XP magnetic beads (Beckman Coulter). Double-sided AMPure cleanup to remove high-molecular-weight fragments was conducted by incubation of double-concentrated AMPure beads added at 0.55x volume to the PCR reactions, followed by cleanup with a 1x AMPure volume. Sequencing libraries were pooled and sequenced on a HiSeq 2500 instrument.


title: in_vivo-matured_SCbeta_ATAC_rep1

value: hPSC-derived beta cell

value: retreived from transplanted mice kidney graft


title: in_vitro-matured_SCbeta_ATAC_12h

value: entrained to circadian metabolic rhythms


title: PH_ATAC_rep1

value: Stage 6 day 15


title: Alpha_ATAC_rep1


title: SCbeta_ATAC_rep1


title: PP2_ATAC_rep1


title: EN_ATAC_rep1

value: hPSC-derived endocrine progenitor

value: Stage 5 day 3


title: 180911_PIKAHIV_gDNA_2B

city: Seattle

first: Molly

last: Ohainle

state: WA

address: 1100 Fairview Ave N, C2-023

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by generation of  fastq files using Illumina's bcl2fastq Conversion Software v1.8.4 (http://support.illumina.com/downloads) /bcl2fastq_conversion_software_184.html).
Reads of low quality were filtered out prior to demultiplexing  using FASTX-Toolkit v0.0.13
Reads were trimmed and aligned to the PIKA HIV guide library using Bowtie v1.0.0, allowing 0 mismatches in the guide sequence, followed by tabulation of read counts using R
Genome_build: PIKA HIV sgRNA Library
Supplementary_files_format_and_content: tab delimited files with read counts for each guide sequence

source_name: THP-1 monocytic cell line

growth_protocol: ZAP-KO THP-1 monocytic cells are grown in RPMI with 10% FBS and Pen/Strep (supplemented to 10mM HEPES, 4.5 g/L D-Glucose, 0.11 g/L Sodium Pyruvate + Glutamax), passaging between 2 x 10^5 cells/mL and 1 x 10^6 cells/mL.

extract_protocol:
Genomic DNA was extracted using a QIAamp DNA Blood Midi kit (Qiagen)
described in samples section individually for each sample
Genomic DNA or reverse-transcribed viral RNA were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All Viral RNA was amplified for each sample where appropriate. For Genomic DNA samples a total of 500-fold coverage of the 15,414 sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For viral RNA, all PCR1 was amplified in the second round. For gDNA, 5uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided SPRI (AMPureXP, Beckman Coulter), quantified with a Qubit HS dsDNA assay and pooled for sequencing.

treatment_protocol: 8 x 10^6 cells (>500X coverage) were transduced with the PIKAHIV library (MOI of 0.75) and selected in 1ug/mL puromycin for 10-14 days. For each replicate, 8 x 10^6 cells were infected with or without overnight IFNα treatment with HIV. Cells and viral supernatants were harvested 3 days post-infection.

value: ZAP-KO THP-1

tag: ifn treatment

value: yes

tag: molecule

value: genomic DNA


title: 180911_PIKAHIV_gDNA_2A


title: 181207_PIKAHIV_gDNA_2


title: B178C23: R2_Input__Naive_WT_For__Ac

city: Paris

first: Sebastian

last: Amigorena

address: 26 rue D'ulm

country: France

institute: Institut Curie

data_processing:
We used all reads with a mapping quality larger than 20 and no duplicated reads. The biological replicates are merged using samtools merge (version 0.1.8)
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.1,0 with the following configurations : Method: Global alignment - 1 mismatch in seed alignment  Algorithm used: Choose uniquely the alignment with the best score
Islands were called using sicer version 1.1 with the following setting: windows size w = 500, gap size g = 1500, FDR = 0.05
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated using sicer version 1.1 and contain the delineation of significant islands

source_name: wild-type

growth_protocol: Naïve CD4 T cells from littermate WT and TRIM28KO mice were enriched by magnetic selection and sorted by flow cytometry.

extract_protocol:
Nuclei were pelleted, washed, and lyzed. Lysates were sonicated to reach fragments of 150 to 500bp.
Immunoprecipitation was performed with H3K9me3 (Abcam) and H3K9Ac (Diagenode). Antibody-bound chromatin was recovered with protein A dynabeads (ThermoFisher)
DNA was eluted, and samples were decrosslinked overnight at 65º, and DNA isolated by phenol/chloroform/isoamyl-alcol followed by QiaQuick PCR purification kit
Illumina TruSeq ChIP library prep kit was used to prepare indexed libraries from IP and Input DNA. Libraries were pooled respecting equimolarity
Sequencing was performed on Illumina HiSeq2500 sequencer in 100bp paired-end reads

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 10 min, quenched with 125mM glycine, washed trice with ice-cold PBS and incubated for 10min in RIPA lysis buffer

tag: strain

tag: genotype

value: wild-type

value: CD4 T cells


title: 181207_PIKAHIV_gDNA_1


title: B178C24: R2_Input_Naive_KO_For_Ac

source_name: Trim28 KO

value: Trim28 KO


title: 180911_PIKAHIV_gDNA_1B


title: B178C20: R2_Input_naive_KO


title: B178C21: R2_Me3_Naive__KO

value: H3K9me3 (Abcam)


title: 180911_PIKAHIV_gDNA_1A


title: PP1_H3K27ac_rep2

value: hPSC-derived pancreatic progenitor 1

value: Stage 3 day 2

value: H3K27ac (Active Motif:39133)


title: B178C22: R2_Ac_Naive_KO

value: H3K9Ac (Diagenode)


title: RED_E1

city: St. Louis

first: Micheal

middle: Benjamin

last: Major

state: MO

address: 4624 Cancer Research Building

department: Department of Cell Biology and Physiology  Department of Otolaryngology

institute: Washington University in St. Louis

data_processing:
read alignment using STAR to hg38, performed by Novogene Corporation
read count per gene quantification, per formed by Novogene Corportaion
filtration of very low expression genes ( defined as less than one count per million in more than 70% of samples)
normalization according to EdgeR R-project package "calcNormFactors" function using "TMM" method, following method of Law et al. F1000Res. 2016; 5: ISCB Comm J-1408.
differential expression analysis using the R-project LIMMA package, using "voom" and "efit" functions, following method of Law et al. F1000Res. 2016; 5: ISCB Comm J-1408.
Genome_build: hg38
Supplementary_files_format_and_content: heatmap_data_BRSK1.csv: normalized filtered log counts per million of genes with significant changes on differential expression
Supplementary_files_format_and_content: heatmap_data_BRSK2.csv: normalized filtered log counts per million of genes with significant changes on differential expression
Supplementary_files_format_and_content: DEG_data_BRISK1.txt: Differentially expressed genes out put form LIMMA
Supplementary_files_format_and_content: DEG_data_BRISK2.txt: Differentially expressed genes out put form LIMMA
Supplementary_files_format_and_content: raw_counts_BRSK2.csv: per gene quantification from Novogene pipeline
Supplementary_files_format_and_content: raw_counts_BRSK1.csv: per gene quantification from Novogene pipeline

growth_protocol: HEK293T cells were cultured in DMEM with 10% FBS in standard incubator.

extract_protocol:
RNA was collected using PureLink RNA Mini Kit (Invitrogen, 12183018A) per manufacturer instruction, and 3ug of RNA was sent for highthorughput sequencing to Novogene Corp.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hcRED, BRSK2, and BRSK1 were overexpressed for 24 hours before collection

tag: genotype/variation

value: hcRED


title: B178C18: R2_Me3_Naive_WT


title: B2_E3


title: Mock_E3

value: Mock


title: B2_E2


title: B176C8: R1_Input_Naive_KO_For_Ac


title: in_vivo-matured_SCbeta_ATAC_rep2

value: HUES 8 hESC line

value: hPSC-derived beta cell

value: retreived from transplanted mice kidney graft


title: Mock_E2


title: B176C7: R1_Input_Naive_WT_For_Ac


title: B1_E3


title: B176C5: R1_Me3_Naive_KO


title: B2_E1


title: B1_E2


title: B176C3: R1_Ac_Naive_WT


title: B176C2: R1_Me3_Naive_WT


title: B176C1: R1_Input_Naive_WT


title: B178C19: R2_Ac_Naive_WT


title: CordBlood1-RNA

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Adapter sequences were trimmed from FASTQs using cutadapt.
Reads were aligned to the hg19 reference transcriptome using STAR two-pass mode
Gene abudances were quantified using STAR geneCounts
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene abdunace counts per-library as described in the data processing steps

source_name: newborn erythroid cells

extract_protocol:
Cells were incubated with 100 μg/ml of cycloheximide (Sigma Aldrich) for 5 minutes at 37°C, washed twice with ice-cold PBS containing 100 μg/ml of cycloheximide and lysed in 10 mM Tris-HCl (pH 7.4), 5 mM MgCl2, 100 mM KCl, 1% Triton X-100, 3 mM DTT, 100 μg/ml cycloheximide, 500 U/ml RNasin (Promega) and 1x Complete Protease Inhibitor, EDTA-free (Roche). Lysates for ribosome profiling were prepared and ribosome protected RNA fragments (RPFs) were isolated as described previouslywith the following modifications: rRNA was depleted using the RiboMinus Eukaryote Kit v2 (Thermo Fisher Scientific) by following the manufacturer’s instructions. rRNA depleted RPFs were purified with the Zymo RNA Clean & Concentrator-5 kit by following the manufacturer’s instructions for small RNAs. PAGE purification of RPFs was performed as described previously and resulting RPFs were dephosphorylated in FastAP mix (19.5 µl H2O, 2.5 µl 10x FastAP buffer (Thermo Fisher Scientific), 2.5 U FastAP enzyme (1 U/µl; Thermo Fisher Scientific), 0.5 µl Murine RNase Inhibitor (New England Biolabs)) and incubating for 20 minutes at 37°C. In the meantime, polynucleotide kinase mix was prepared (57 µl H2O, 10 µl 10x PNK buffer (New England Biolabs), 0.5 µl Murine RNase Inhibitor, 6.5 µl T4 PNK (10 U/µl; New England Biolabs), 1 µl TURBO DNase) and added 75 µl to each 25 µl sample and incubated 20 minutes at 37°C. RPFs were purified with the Zymo RNA Clean & Concentrator-5 kit following the manufacturer’s instructions for small RNAs.
RNA was eluted in 7 µl H2O, 1.5 µl DMSO and 10 pM 3’ adapter (/Phos/AGATCGGAAGAGCACACGTCTG/ddC) were added before denaturation at 65°C for 2 minutes and transferring samples to ice. Subsequently, 11 µl ligation mix was added (2 µl 10x T4 RNA ligation buffer (New England Biolabs), 0.3 µl DMSO, 0.2 µl ATP, 0.3 µl RNAse inhibitor, 7 µl 50% PEG 8000, 1.2 µl T4 RNA Ligase 1 High Concentration (New England Biolabs)) using low retention pipette tips and incubated 1 hour at 23°C with agitation. Ligation reactions were purified to remove free 3’ adapter using Silane bead purifications. For each reaction, 15 µl Silane beads (Thermo Fisher Scientific) were washed twice in 1 ml RLT buffer (Qiagen), beads were resuspended in 60 µl RLT, and 60 µl beads in RLT was combined with 20 µl ligation reaction. 0.7 volumes 100% ethanol were added and incubated for 10 minutes at room temperature. Supernatant was removed and beads were washed twice with 70 % ethanol before eluting air-dried beads in 10 µl H2O. Next, 10 pM reverse transcription primer (/5’biotin/GACGTGTGCTCTTCCGA) was added and samples were denatured at 72°C for 3 minutes before transferring to ice. To each reaction 7 µl reverse transcription mix (0.25 µl H2O, 2 µl 5x Smartscribe first strand buffer (Takara), 0.25 µl RNase inhibitor, 2 µl Smartscribe RT (Takara), 2 µl dNTP, 0.5 µl 20 mM DTT) were added and samples were incubated at 42°C for 15 minutes. Next, 2 µl template-switching oligo (5'biotin/TACACGACGCTCTTCCGATCTrGrG+G) were added and samples were incubated 90 minutes at 42°C, followed by 10 minutes at 70°C. Samples were purified with Silane beads and subjected to PCR amplification using 2x NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs) as described previously. Amplicons migrating at a size of ~157 bp were subjected to two consecutive rounds of gel purification. For preparation of mRNA sequencing libraries, total RNA was extracted with the Direct-zol RNA MiniPrep Plus Kit (Zymo Research) according to the manufacturer’s instructions. Total RNA was poly-A selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) according to the manufacturer’s instructions. mRNA was eluted in 27 µl H2O, 3 µl 10x FastAP buffer were added and RNA was heat fragmented for 3 minutes at 91°C. Fragmented RNA was end-repaired, adapter ligated, reverse transcribed and PCR amplified.

treatment_protocol: CD34+ HSPCs from adult and newborn were differentiated until day 7 (proerythroblast stage) for examining ribosome profiles.

value: hematopoetic cells

value: newborn erythroid cells


title: A629T34: D0_KO3

data_processing:
Sequences were aligned with STAR and counts were generated by HTSeq using the annotations from mm10.
Raw counts were normalized to log2 transformed Counts using DESeq2
Genome_build: mm10

extract_protocol:
After phenol chloroform addition and centrifugation, aqueous phase was collected, mixed with ethanol, and transferred to miRNeasy columns.
RNA was extracted according to manufacturer's instructions. Eluates were digested with TurboDNAse (thermofisher) prior to further analysis.
Illumina HiSeq library prep kit was used to prepare the library.
Sequencing was performed on Illumina HiSeq2500 sequencer in 100bp paired-end reads

treatment_protocol: Cells were lysed in Trizol.


title: CordBlood4-RNA


title: B178C17: R2_Input_Naive_WT


title: CordBlood2-RNA


title: A629T33: D0_KO2


title: Adult4-RNA

source_name: adult erythroid cells

value: adult erythroid cells


title: A629T32: D0_KO1


title: Adult3-RNA


title: A629T30: D0_WT2


title: Adult1-RNA


title: A629T29: D0_WT1


title: A629T31: D0_WT3


title: CordBlood4-ribosomeprofiling

data_processing:
Library strategy: Ribo-seq
Adapter sequences were trimmed from FASTQs using cutadapt.
Reads were aligned to the hg19 reference transcriptome using STAR two-pass mode
Gene abudances were quantified using STAR geneCounts
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene abdunace counts per-library as described in the data processing steps


title: B176C4: R1_Input_Naive_KO


title: CordBlood-Rep1 (RNA-Seq)

data_processing:
Adapter sequences were trimmed from FASTQs using trimmomatic
Transcript pseudocounts were estimated using kallisto v0.4.4 for a 31-mer index built on hg19
TPM counts at the gene level were estimated using sleuth
Genome_build: hg19
Supplementary_files_format_and_content: TPM count estimates are assembled in a matrix

source_name: CD34+ hematopoetic cells differentiated

growth_protocol: CD34+ HSPCs from various stages were cultured in a three-stage erythroid differentiation culture system that we have previously described30. Briefly, the cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Life Technologies) containing 2% human AB plasma, 3% human AB serum, 1% penicillin/streptomycin, 200 μg/mL human holo-transferrin, 3 U/mL heparin, and 10 μg/mL insulin (base medium). In Phase I (day 0-7), the cultures were supplemented with erythropoietin (EPO) (3 U/mL), stem cell factor (SCF) (10 ng/mL), and interleukin 3 (IL-3) (1 ng/mL), and in Phase II (day 7-12), they were supplemented with EPO and SCF alone. In Phase III (day 12 onwards), primary cell cultures contained 1mg/mL human holo-transferrin and were supplemented with EPO. Cell counts were measured either using a Beckman Coulter automated cell counter or manually with a hemocytometer. Cells were maintained between 105-106 cells per mL in Phases I and II, and at 106 cells per mL in Phase III. Cells were split into fresh culture medium every 3 days in this culture.

extract_protocol:
NA
Illumina Truseq

tag: developmental stage

value: newborn


title: CordBlood-Rep2 (RNA-Seq)


title: CordBlood2-ribosomeprofiling


title: B1_E1


title: B176C6: R1_Ac_Naive_KO


title: AdultBlood-Rep2 (RNA-Seq)

value: adult


title: AdultBlood-Rep1 (RNA-Seq)


title: CordBlood1-ribosomeprofiling


title: RED_E3


title: Adult4-ribosomeprofiling